Install PyHDF on CentOS7

Question

Please help,

I am having trouble to install pyhdf on CentOS7. I should say, I am a newbie to linux

Pyhdf needs HDF to be installed and so far I've tried the following:

1. first install HDF with ./configure, gmake && gmake check. However, check exit with 6 errors.

2. Then I used "yum install hdf-devel" This way, HDF got installed on the computer but pyhdf still exists with errors. As for the phydf I tried both "pip install pyhdf" and "python setup.py install" but always end up unsuccessful. Please see the log below for details. Thank you!

   $ python setup.py build running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "pyhdf._hdfext" sources build_src: building npy-pkg config files running build_py running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'pyhdf._hdfext' extension compiling C sources C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -I/opt/rh/rh-python36/root/usr/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -std=c99

   compile options: '-I/usr/local/hdf4/include -I/home/npec/oop/oop_venv/lib64/python3.6/site-packages/numpy/core/include -I/home/npec/oop/oop_venv/include -I/opt/rh/rh-python36/root/usr/include/python3.6m -c' extra options: '-DNOSZIP' gcc -pthread -shared -L/opt/rh/rh-python36/root/usr/lib64-Wl,-z,relro -Wl,-rpath,/opt/rh/rh-python36/root/usr/lib64 -Wl,--enable-new-dtags build/temp.linux-x86_64-3.6/pyhdf/hdfext_wrap.o -L/usr/local/hdf4/lib -L/usr/local/jpeg/lib -L/usr/local/zlib/lib -L/usr/local/jpeg/lib -L/usr/local/zlib/lib -L/usr/local/szip/lib -L/usr/lib -L/usr/local/lib -L/lib -L/opt/rh/rh-python36/root/usr/lib64 -lmfhdf -ldf -ljpeg -lz -lpython3.6m -o build/lib.linux-x86_64-3.6/pyhdf/_hdfext.cpython-36m-x86_64-linux-gnu.so /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(mfsd.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(putget.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(putgetg.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(string.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(var.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(array.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(attr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(cdf.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(dim.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(file.o): relocation R_X86_64_32 against undefined symbolrlim' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(hdfsds.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(iarray.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(error.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(nssdc.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(xdrposix.o): relocation R_X86_64_32S against .data' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(cszip.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dfconv.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dfgroup.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dfknat.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dfkswap.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(hblocks.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(hchunks.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(hcomp.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(herr.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(hextelt.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(hfile.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(hfiledd.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(mcache.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(mfan.o): relocation R_X86_64_32 against symbol ANIanncmp' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(mstdio.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(tbbt.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(vattr.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(vg.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(vgp.o): relocation R_X86_64_32 against symbolvdestroynode' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(vhi.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(vio.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(vparse.o): relocation R_X86_64_32S against .bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(vrw.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(vsfld.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(atom.o): relocation R_X86_64_32S against.bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(bitvect.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(cdeflate.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(cnbit.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(cnone.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(crle.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(cskphuff.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dynarray.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(glist.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(hbitio.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(hbuffer.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(hcompri.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(vconv.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dfcomp.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dfimcomp.o): relocation R_X86_64_32 against.bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dfjpeg.o): relocation R_X86_64_32S against symbol hdf_init_destination' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dfrle.o): relocation R_X86_64_32S against.bss' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libdf.a(dfunjpeg.o): relocation R_X86_64_32S against symbol hdf_init_source' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcapimin.o): relocation R_X86_64_32 against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcapistd.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcparam.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcinit.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcmaster.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcmarker.o): relocation R_X86_64_32S against symbol jpeg_natural_order' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcmainct.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcprepct.o): relocation R_X86_64_32S against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jccoefct.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jccolor.o): relocation R_X86_64_32S against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcsample.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jchuff.o): relocation R_X86_64_32S against symbol jpeg_natural_order' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcphuff.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcdctmgr.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jfdctfst.o): relocation R_X86_64_32 against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jfdctflt.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jfdctint.o): relocation R_X86_64_32 against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdapimin.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdapistd.o): relocation R_X86_64_32 against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdmaster.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdinput.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdmarker.o): relocation R_X86_64_32S against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdhuff.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdphuff.o): relocation R_X86_64_32S against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdmainct.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdcoefct.o): relocation R_X86_64_32S against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdpostct.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jddctmgr.o): relocation R_X86_64_32 against symbol jpeg_idct_2x2' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jidctfst.o): relocation R_X86_64_32 against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jidctflt.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jidctint.o): relocation R_X86_64_32 against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jidctred.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdsample.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdcolor.o): relocation R_X86_64_32S against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jquant1.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jquant2.o): relocation R_X86_64_32S against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jdmerge.o): relocation R_X86_64_32S against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jcomapi.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jutils.o): relocation R_X86_64_32 against.text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jerror.o): relocation R_X86_64_32S against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jmemmgr.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libjpeg.a(jmemnobs.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libz.a(deflate.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libz.a(inflate.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libz.a(inftrees.o): relocation R_X86_64_32S against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libz.a(trees.o): relocation R_X86_64_32S against .data' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libz.a(zutil.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libz.a(adler32.o): relocation R_X86_64_32 against .text' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libz.a(crc32.o): relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: /usr/local/hdf4/lib/libz.a(inffast.o): relocation R_X86_64_32S against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: Nonrepresentable section on output collect2: error: ld returned 1 exit status error: Command "gcc -pthread -shared -L/opt/rh/rh-python36/root/usr/lib64-Wl,-z,relro -Wl,-rpath,/opt/rh/rh-python36/root/usr/lib64 -Wl,--enable-new-dtags build/temp.linux-x86_64-3.6/pyhdf/hdfext_wrap.o -L/usr/local/hdf4/lib -L/usr/local/jpeg/lib -L/usr/local/zlib/lib -L/usr/local/jpeg/lib -L/usr/local/zlib/lib -L/usr/local/szip/lib -L/usr/lib -L/usr/local/lib -L/lib -L/opt/rh/rh-python36/root/usr/lib64 -lmfhdf -ldf -ljpeg -lz -lpython3.6m -o build/lib.linux-x86_64-3.6/pyhdf/_hdfext.cpython-36m-x86_64-linux-gnu.so" failed with exit status 1

Answer 1

This is not an answer, per se, to the questions raised, but provided me a way out of trouble.
I wish I knew it right away.

To get pyhdf up and running I just set up anaconda environment. Details on setting up conda environment is available at the official Anaconda website. Massive thanks to Anaconda Team

From there, everything is just as simple as pip/conda install

Being new to Linux environment can be frustrating, but once everything is set, the joy comes.